[Chimera-users] regarding to minimization and preparation of sdf files for docking.

[Elaine Meng]

Hi Prasad,
You would have to ask a specific question — we cannot go through all the molecules individually and perform in-depth consulting on your individual research project.  We don’t have funding for that kind of support.

I looked at the logs and mostly see just messages (not problems) except one message where the hydrogens weren’t added to one atom.  It may be that almost all molecules are processed just fine, and that the structure of that one molecule is strange somehow.  I don’t know.  If you have a specific molecule that has a specific problem, you could use menu: Help… Report a Bug and attach the structure and describe all the steps needed to reproduce the problem.

I hope this helps,
Elaine
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Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 2, 2019, at 1:20 AM, prasad ssv <prasad.ssva at gmail.com> wrote:
> 
> hi,
> i had a database which contains a set of molecules,all molecules in sdf format i would like to minimize all sdf files and dock preparation.can you please help me do that.
> i had performed dock prep for those sdf files but it showing some reply log and bugs.when i am adding hydrogens it is gvng reply log as attached in below files.
> can you please go through and suggest me a solution.
> thanking you,